The Whooves Collection Ep3: The Crystal Shadows
by The Writer in Black
Summary: Twilight has fallen through the time vortex and has been transported back to the Crystal Empire under the reign of the malicious King Sombra. The Doctor comes to her aid, but finds that the Empire holds a dark secret. With the help of a mysterious stallion and his numbers, the Doctor and Twilight face off against Sombra and one of the universe's deadliest foes: the Vashta Nerada.
1. Introduction

_A/N: The third episode cometh! I can now guarantee that chapters will be longer. The down side to this is that they may take more time to write. Hopefully all you readers have the Element of Patience. Anyway, everypony... on with the story!_

* * *

**_The Whooves Collection: Episode 3_**_**  
**_

**_The Crystal Shadows_**

**_Introduction_**

_**=All Information Unknown=** _

"Why do I have to stay out of the shadows?" Twilight peered into the darkness to get a better look at the figure, but all she could see through the inky blackness was a blurred form at the back of the cave. "Are you alright?" Twilight asked him.

He turned to face her, and then he looked back to the floor. "What do you think?" he said quietly. His tone sounded harsh and hateful to Twilight.

Twilight used her magic to conjure up an illumination spell and increased her visibility. Now that she had better lighting, she could get a better glimpse of this mysterious pony. What Twilight saw made her lose concentration briefly, the light flickering. The eyes belonged to a pegasus stallion lying huddled in the corner of the, now easily recognizable, cave. He seemed to be in his twenties, had a grey coat that was almost charcoal colored, and a black mane with a thin golden streak in the back. Twilight paid little attention to his appearance because she was focusing more on the wounds that he had.

The stallion had multiple cuts and scars along his body, with dried blood sticking to his messy coat. Some places were bandaged crudely, leading Twilight to believe that he did them on his own. One bandage on his left foreleg stood out more than the rest, though. Twilight examined it further and saw that the area closer to his hoof was bulging slightly.

Twilight began to advance slowly, but the stallion cringed when she came close. Twilight noticed how this reaction looked similar to when she and Fluttershy would occasionally find animals near the Everfree Forest that had sustained identical treatment to the stallion. Twilight then understood that the pegasus wasn't just frightened, but that he was downright terrified of her!

"Stay away from me," the stallion ordered. "I've experienced enough pain today!"

Twilight pulled back quickly at the sudden outburst, but at least she knew why the stallion was afraid of her. Somepony, or more, had been torturing him, which would explain the wounds. Twilight tried to get closer again, but the stallion just cowered in fear.

"I'm not going to try to hurt you," Twilight said in what she hoped was a soothing tone, "I just want to help you."

The stallion said nothing, but gave her a piercing glare. Twilight was able to reach him without any further problems, and she then proceeded to examine his cuts and scars along his body. Twilight thought back to her studies on magical healing and tried helping to heal some of the pony's injuries. Instead of resisting her, he just gave her a look of bewilderment.

"Why are you doing this?" he asked her.

"What do you mean?"

"No pony has ever tried... _helping me_ before. They only inflict pain. That's all anypony does. Ever."

The last word was said so quietly that Twilight almost missed it, but that word made her realize something.

This stallion hadn't seen _any_ kindness in Celestia knows _how_ long!

"Fluttershy would have a heart attack."

"What?" the stallion asked.

"Sorry," Twilight apologized, "I was thinking aloud."

"Oh."

Twilight finished fixing some of the stallion's more prominent scrapes and most of the smaller cuts.

"I don't think that we've been formally introduced." Twilight held out a hoof, "I'm Twilight Sparkle."

The stallion slowly accepted Twilight's outstretched hoof. "My name is... Jonathan. Or at least I think it is," he added. "How did you get down here?" Jonathan asked her.

"Well... I was with the Doctor and... and then we..." she thought for a moment. "I don't know how I got here."

"Figures." the stallion sighed, "I'm here because-"

Hoofsteps echoed throughout the cavern and Jonathan froze. "They're coming. Turn off that light," he hissed at Twilight, "and hide in the corner!"

"Wait. You said to stay out of the shadows."

"I know, but maybe they won't hurt you."

The hoofsteps were growing louder as they drew closer to where they were hidden. Twilight did as she was told and hid, just in time, too. A large section of the far wall was pulled away and two guards, covered in armor, entered the room. They stepped to the side and allowed another figure to enter. Twilight had to prevent herself from crying out.

The mysterious figure was King Sombra.

Twilight watched as he approached Jonathan, glaring at him with cold, calculated hate.

"Yes, Your Majesty?" the stallion asked Sombra, head lowered.

"What do you have for me today, boy."

Jonathan walked over to another side of the room and grabbed a torn piece of paper in his mouth. He returned to Sombra and gave him the sheet. Sombra used his dark magic to pick it up and read it.

"Can't you do anything right?" he growled.

"I'm sorry. It's the best I can do, Your Majesty," Jonathan said without looking up.

"I'm well aware." Sombra turned around and strolled out of the cave, flanked by his guards. The wall returned to it's original position and the hoofsteps began to recede.

When there was silence, Twilight used her horn to create a ball of light that floated at the ceiling of the chamber. She looked over to Jonathan and watched him walk over to a stack of papers in the corner. He picked up a piece of chalk in his hooves and turned to the wall, using it to write a line on the wall and set the chalk back down, next to the papers.

"What was that-" Twilight stopped and looked at the wall. Then she looked at the one next to her, and then to the other two.

Every space along the walls, and the ceiling, of the cell were covered in numbers.

"... about?" Twilight finished her question. She stared at all the walls for a few more minutes. Just then, Twilight remembered what the Impostor had said on her first journey.

_"... the numbers will find you, Doctor. They will find you..."_

Twilight looked at Jonathan, who said, "This is why I'm here."

_"... They will find you."_

* * *

_A/N: This is probably going to be the longest intro I'll ever write for my Whooves series. Ever. Still, I could be wrong._

_ The next chapter will be coming in less than a week, or a week at most._


	2. Whispers in the Dark

**_Chapter 1_**

**_Whispers in the Dark_**

**Somewhere in the Time Vortex; TARDIS; Control Room**

_VVRROOMMP! VVRROOMMP! VVRROOMMP! VVRROOMMP!_

"Come on! Work for me here!" the Doctor shouted at the TARDIS.

The TARDIS jolted to the left in response, flinging the Doctor into one of the twisted pillars.

"How rude!" the Doctor groaned as he picked himself back up. He made it to the control panels and checked his progress on the monitor. "Almost there! I'm coming Ms. Sparkle!"

Suddenly, the monitor screen began flashing and dozens of images appeared and disappeared within seconds.

"What the-?"

The screen blackened and a number sequence popped up digitally: 4, 1, 8, 3, 0. Then, as suddenly as they appeared, they vanished.

_VVRROOMMP! VVRROOMMP! VVRROOMMP!_ The TARDIS came to a bumpy halt and the Doctor raced to the doors. He threw them open and ran into Twilight. They tumbled on the ground and landed side by side.

"Doctor!" Twilight cried.

"Twilight!" the Doctor exclaimed.

"Doctor?" Jonathan said.

Twilight and the Doctor jumped to their hooves and began talking rapid fire.

"You made it!" Twilight said.

"I did!"

"How did I get here and how did you find me?"

"Long story. Better for another time." The Doctor approached Jonathan and asked him, "Who are you?"

"I- I- I'm Jon- Jonathan," he stammered.

"Were you holding Ms. Sparkle here hostage? Hmm?"

Twilight stepped in, "No he wasn't, Doctor. He's a friend. _He's_ the one being held against his will."

"Oh, well then. I guess I can rescue both of you!" The Doctor smiled gleefully, "That's a plus. Now, come on! Into the TARDIS, both of you!" The Doctor turned back to the TARDIS, but it was gone. The Doctor stood there with his mouth hanging open. "What?! WHAT?!"

The Doctor was about to step forward when Jonathan grabbed him from behind.

"DON'T!" he yelled.

The Doctor got out of Jonathan's grip and turned to face him. "Don't what?"

Jonathan pointed at a patch of shadow that spread out about a foot in front of the Doctor. "Don't touch the shadows."

The Doctor looked between the shadows and Jonathan, his expression deadly serious. "What about the shadows?" he questioned, voice lowered.

"Don't touch them. They'll hurt you."

The Doctor pulled out his Sonic Screwdriver, held it in his mouth, and scanned the shadow in front of him. "Not here," he pleaded, "Not now!"

"What's wrong with the shadows, Doctor?" Twilight asked him.

"Everything."

"Everything, what?"

The Doctor turned to Twilight. "Every species has had an irrational fear of the dark for almost all of time," he said, "but it's not irrational. They've been afraid of what's in the dark. The Vashta Nerada."

"The Vashta what?" Jonathan said.

"Vashta Nerada," the Doctor corrected, "They're microscopic, flesh-eating creatures that are in the dark. Very hard to spot, but you can see them sometimes. Like.. the bits of dust in sunbeams."

Twilight stared at the shadows. "Have you faced them before?"

"Yes," the Doctor said distantly. He began thinking back to The Library and his confrontation with them. The Doctor came back to the real world and felt somepony shaking him.

"Doctor?!" Twilight's voice was suddenly panicked and fearful.

The Doctor shook his head to clear it and was able to say, "Wha-?!"

"The shadows," Jonathan said, "They're coming."

The Doctor looked at the shadow and watched it inch towards them, slowly.

"Back away!" he ordered, "Quickly!"

The three ponies stepped away from the shadow and ran into the wall.

"Is there an exit?!" the Doctor shouted.

"Only the one directly behind us," Jonathan answered, "but it's magically sealed."

"Good enough!" The Doctor spun around and pointed his Screwdriver at the wall and it slid open. "Go, now!"

"Wait!" Jonathan ran over to his stack of papers and proctored a notebook from under it. He grabbed it in his mouth and ran out of the cell. The Doctor and Twilight were on the other side of the door, and the Doctor sealed it as Jonathan jumped through. Outside of the cell was a large staircase that spiraled upward. Twilight was looking up

"What was that about?!" the Doctor demanded an explanation.

Jonathan was breathing heavily and staring at the door. "They never do that," he muttered, "never..."

"Why did you go for the book?!"

Jonathan placed it on the floor and opened to the first page. The Doctor looked over it and his eyes widened.

"The numbers, Doctor," Twilight said, "Remember what that mirror creature said about the numbers?"

The Doctor nodded quickly and turned to Jonathan. "You need to come with us. Now." The Doctor began to trot up the large spiral staircase, Twilight following behind. Jonathan looked back to the door and watched some shadowy tendrils begin to pour through any available cracks in the wall.

"Wait for me!" Jonathan shouted up the steps. He grabbed the book in his mouth and raced after Twilight and the Doctor.

As the sounds of his hoofsteps faded away, the misty tendrils of shadow began to form into the shape of one of the armored guards.

_"Find them,"_ it hissed, _"and inform the Master of their prescence."_

The guard's body dissolved, and the shadows began advancing up the stairs in pursuit of the trio.

**Gaia; Equestria; Crystal Empire; Sombra's Throne Room _=Year_**_** Unknown=**_

Sombra stood on the balcony, overlooking his empire and its inhabitants. He watched as dozens of chain bound ponies struggled to work and harvest the crystals that this region of the land was best known for. He watched one of the slaves struggle under the load of a mine cart filled to the brim with crystals that needed to be shined. Sombra laugh was a deep, throaty sound that was mixed in with the growl of a panther. Sombra smiled the slave's pain as he pulled the cart, and it looked wonderful to behold.

_"Master?"_

Sombra turned from his viewpoint to face one of his shadow guards. "What is it?"

_"The nameless one has escaped,"_ the guard hissed.

"How is such a thing possible?!"

_"It is them. The Wandering One and the_ _Traveler,"_ the guard flinched after he said those words, as if they physically hurt him.

Sombra turned back to look at the Empire and addressed the guard, "Bring them here, immediately. But make them... comfortable. I wish to know their purpose in my realm." Sombra didn't need to turn around to know that the shadow departed. He knew it left, he _felt_ it leave.

**Gaia; Equestria; Crystal Empire; Lower Caverns; _=Year Soon to be Revealed=_**

"Doctor?"

"Yeth?" he answered through his teeth. He was holding the Sonic Screwdriver in his mouth and scanning the path ahead of them for any Vashta Nerada. Luckily, the passages were lit with enchanted torches that were charmed so that they would never go out, according to Twilight.

"Would you happen to know _when_ we are?" she asked.

The Doctor proceeded to scan the tunnels, but spoke between button pressing. "I would geth that from the shmell that we're about... one thousand... _tree_ yearsh before we left your library."

"One thousand three years..." Twilight calculated, "... that means that we're in year one Pre-Celestian Era!"

"Whath?" the Doctor said through the Screwdriver.

"We're one year before Princess Celestia banishes Nightmare Moon to the moon and begins ruling Equestria on her own."

"Huh!" the Doctor remarked, "When we find the TARDIS, you should tell me more about your country's history. It may come in handy in the future."

"Or the past," Twilight joked. "Wait. How are we going to find the TARDIS, exactly?"

"There's a tracking device inside of the TARDIS that is connected to my Sonic Screwdriver. With this thing, I'll never lose the TARDIS. It's even more useful when I forget where I park!"

Jonathan listened to the two of them converse as he followed behind. He would occasionally glance behind him to see if any guards were following them, and to check on his book, which he had skillfully balanced on his back. Jonathan began to think about what the stallion who called himself the Doctor, and Twilight, were talking about. It didn't seem like a normal discussion, all the terms they were using: Pre-Celestian Era, _when_ they were, able to tell what year it was by smell. He was so caught up in his thoughts that he didn't notice Twilight walking next to him.

"Are you alright?" she asked him, bringing him back to the real world.

"Huh? Oh, yeah. Fine."

"Are you sure?"

Jonathan looked towards the Doctor, scanning the pathways "No," he admitted, "I'm not."

"What's wrong?"

"Everything. Everything's wrong. The biggest thing is that I'm escaping from a dungeon and an evil unicorn dictator, while at the same time I'm being rescued by two strange ponies who suddenly come out of nowhere! That, and the fact that I've just realized that I have absolutely no clue who the hell I am!"

Twilight's expression became one of confusion, "You don't know who you are?"

"I don't think that Jonathan is actually my real name," he said, "and I only remember being trapped down there for about three or four years. Still, it could have been longer."

"I'm sorry about what you've been through," Twilight said softly, "I truly am."

"I know you are. I could tell when you helped me with my injuries. You are the only pony that I can think of that's ever shown me kindness." Jonathan and Twilight walked in silence, the Sonic Screwdriver's buzzing breaking it occasionally.

"What about you two?" Jonathan nodded towards the Doctor, "Are you two..."

"Oh, no!" Twilight said quickly, "We're not a couple! At all."

"Oh, okay. Yeah, I was wondering."

_"Jonathan..." _a voice called out.

"What?!" he spun around, peering into the tunnel, "Who's there?!"

"What do you mean?" Twilight mimicked Jonathan. "There's nopony there."

_"We miss you, Jonathan..."_ it was a mare's voice as far as he could tell.

Jonathan looked down another passage, his eyes searching through the darkness.

_"Come back to us..."_ the voice began to fade.

"Jonathan!" Twilight shouted.

Jonathan opened his eyes and found himself standing a few inches away from the line of a shadow. "GAH!" he cried out and he stumbled backwards. "What happened?!" Twilight and the Doctor were standing over him, Twilight looking down and the Doctor looking at the shadow in front of the tunnel.

"You started to walk towards that tunnel," Twilight explained, "but you were sort of... dazed... when you did it."

Jonathan turned back to look at the tunnel, but all that he saw was the darkness within it. He was panting, "I... heard... somepony... calling... me."

"Nopony was there."

"No," the Doctor spoke for the first time in a while, "Some_thing_ is."

A light wind began to blow through the tunnels, creating a low howl. The three ponies looked around and saw tendrils of shadow approaching them from behind. There was another set of them coming out of the tunnel that they were facing.

"Doctor," Twilight said uneasily, "what do we do now?"

"Uhh... we run."

"Run?!"

"Yes," the Doctor confirmed, "RUN!"

Twilight and the Doctor turned and ran while Jonathan grabbed his book and did the same. They raced through the twisted corridors, ran down narrow passageways, and went up and down some sloped tunnels. The shadow creatures following them the whole way.

_"Halt!"_ some of them hissed loudly.

"Did it just tell us to halt?!" the Doctor exclaimed.

"Yes!" Jonathan shouted back.

"They shouldn't be able to do that!"

"Can we finish this later?! After we're done running!" Twilight ordered.

Suddenly, a wall of shadow rose up in front of them, making them slide to a halt. The shadow wall began to melt down and take the form of the guards, almost a dozen of them.

_"You will come with us."_

The trio turned around, but found themselves surrounded. The Doctor straightened up and addressed the creatures, "Come with you, eh? Why not kill us? Isn't that what you do?"

_"The Master requests your presence,"_ one of the guards replied.

"Who is your Master?" the Doctor asked.

One of the creatures, larger then the others, stepped forward. _"Our Master brought us here. He helped us. We serve him proudly and diligently, for he is our rescuer."_ The head guard approached the Doctor and they stood face to face. _"You must come with us."_

The guard grabbed the Doctor's face and he fell to the floor, unconscious.

"Doctor!" Twilight cried as she rushed to his aid.

A guard came up behind her and she fell to the ground as well.

Jonathan braced himself, waiting for the guards to get him.

The leader approached him and looked him over. _"The Master wishes for you to be unharmed. We cannot damage his possessions."_

"That hasn't stopped you before!" Jonathan spat.

_"I suppose I can make an exception."_ The guard punched Jonathan's face and he was out before he hit the floor.


	3. Honored Guests

_A/N: It took me two weeks, but I finished this chapter. Sorry to keep you all waiting. Onwards and upwards!_

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_**Chapter 2  
**_

_**Honored Guests**_

**G****aia; Equestria; Crystal Empire; Crystal Palace; Main Dining Hall; 1 P.C.E.**

Twilight groaned as she shook off her sleepiness and woke up. Twilight opened her eyes slowly and processed where she was. She was sitting on the floor, but her head was lying on a large table that was inside of a massive room, nearly five stories high and one hundred feet long. The space was lit with dozens of the charmed torches, similar to the ones from the caverns. She turned and saw the Doctor to her left, waking up as well. She looked to her right and saw Jonathan lying on his side in a far corner of the room, his legs in chains, and still unconscious. There was also a bit of red that had come out of the corner of his mouth that Twilight instantly recognized as blood. She started to get up, but a pain in her head stopped her.

_"They are_ waking," a guard's raspy voice said,_ "Inform the Master."_

"What...?" Twilight mumbled, "What's going on?"

"We seem to be inside of a large receiving room!" the Doctor's head shot up off of the table, startling Twilight. "It seems to be approximately thirty-five feet high, one hundred two feet long, twenty feet high, and made out of a sort of gem," the Doctor licked the table, "and... it's not diamond. Perhaps it's quartz! Too bad, I really like diamonds."

"Were you awake this whole time?!" Twilight exclaimed.

"No. I just gathered information from my surroundings just now."

"You're crazy," Twilight said.

"So I've been told," the Doctor replied jokingly.

_"The Master is coming,"_ a guard standing behind them interrupted. _"You shall respect the Master. Speak only when spoken to, and do not interrupt."_

"And do we have to refer to him as 'Great One' as well?" the Doctor asked snidely. Twilight snickered at his remark.

The guard growled menacingly, but stood erect when he heard the large double doors at the end of the room open. Twilight cringed when a black-coated unicorn stallion with a curved, red horn and wearing polished metal armor with a blood-red cape entered the room.

"Ah... the infamous Wandering One," King Sombra greeted the Doctor in his deep, growling voice, "I have heard much of your travels."

"Have you now?" the Doctor was intrigued.

"That's Sombra," Twilight whispered loud enough for the Doctor to hear.

"I see why you don't like him," the Doctor whispered back, "he looks rather threatening."

"My apologies for the guards," Sombra continued, "but I doubted that you would go with them willingly. Still, I hope there were no inconveniences."

"Oh, not to worry, good sir. I've been in worse scenarios."

"I see." Sombra sat at the end of the large table and looked to the Doctor, "The point is that I wanted to greet you and your... associate," he glanced over at Twilight. "When I heard of your arrival, I sent my men to find you, but I guess that you met _him_..." Sombra gestured to the passed out Jonathan, and both Twilight and the Doctor turned towards him.

"What...?" Jonathan said through his unconscious state, "Who are you...?"

"He's not very sane, I'm afraid. He was spouting nonsense when we brought him to the caves. He's been slipping in and out of sanity daily. So much so, that I'm surprised he hasn't dropped dead from it."

"That's terrible," the Doctor remarked, "perhaps I should examine him."

"No!" Sombra said a little too loudly. "No," he said quieter than before, "that won't be necessary."

"Are you certain?"

"Yes," Sombra confirmed, "I have someone that monitors his cell each day."

"I must have missed him," the Doctor hinted at disbelief, "I would like to see what observations he's made."

"Would you now?" Sombra said with a slight edge to his voice, "I'll... see if he's around."

Twilight eyed Sombra suspiciously as he spoke. She knew that whatever he was telling them were lies, and she guessed that the Doctor sensed this as well, judging by the way he challenged each statement. She leaned towards the Doctor and whispered, "This isn't right. Celestia described him as evil and cruel, and I even fought him. He was never known for being, well... _this_."

One of Sombra's guards came over to him and whispered something into his ear. The Doctor used this moment to reply to Twilight's comment. "I know what you mean. But one thing I've learned is that anyone- sorry... anypony with this much nice must be hiding something."

"Excuse me," Sombra said. The Doctor and Twilight faced him quickly, ending their conversation abruptly. "I must apologize, but a small matter has arisen that I must attend to immediately." He stood up to the table and said to the Doctor, "If you could please see me when you are finished. My guards shall direct you to my quarters." Sombra turned and left the dining hall, each the guards flanking him.

When the doors closed and the hoofsteps receded Twilight turned to the Doctor, and both of them turned to Jonathan.

"I'll check on him," Twilight said.

"Same here," the Doctor agreed.

Twilight and the Doctor hurried over to him. While Twilight began to heal the remainder of Jonathan's wounds, the Doctor pulled out his Screwdriver and scanned him.

"Jonathan?" Twilight asked him, "Jonathan? Can you hear me?" Twilight placed a hoof on his forehead and her vision went black.

* * *

_"The spell placed upon you has been weakened."_

_Twilight looked around in the inky blackness, searching for the voice. "Hello?" she called out, "Is anypony there?"_

_"What spell?" Jonathan's voice came from somewhere to Twilight's right. "I don't understand."_

_Twilight turned to find Jonathan standing a couple feet away from her, staring into the void. "Jonathan!" she shouted to him._

_"The spell that has forbidden you from remembering," the first voice sounded again. It was distinctly male, and it was sort of light and welcoming._

_Twilight began walking towards Jonathan, and as she approached him, she saw a thin image of a strange creature, but it was emitting a bright light that prevented her from discern any physical characteristics other than a pair of eyes and a head. When she reached Jonathan, Twilight was able to see the image more clearly. What looked to be a three-dimensional creature was actually a two-dimensional projection._

_"Remembering what?" Jonathan asked it._

_Twilight watched as the creature looked down slightly. "Remembering your past. Your life. Who you were before the numbers."_

_Jonathan's eyes brightened, "You know about them?! Why I see them?!"_

_"Of course."_

_"How?"_

_"It was a mistake. It was never supposed to happen." The creature's head shot up and looked towards the area behind him. He turned back to Jonathan, "I don't have enough time to explain, but I can help you in your present situation." The projection walked up to Jonathan and touched his head. Jonathan's eyes rolled back into his head and he gave a soft moan before falling to the floor._

_Twilight tried to help, but all she made contact with was empty air, as Jonathan's body dissolved into mist. When Twilight looked back at the image, she gave a small shriek, the eyes were staring straight at her._

_"I've done as much as I can, for now," the creature said to her, "it's all up to you three. Four, one, eight, three, zero"_

_"What?" Twilight asked._

_"I can say no more. Or in the Doctor's words: 'Spoilers.'"_

_The image faded and the dark void began to melt away. "Wait!" Twilight called out, "Come back!"_

_"Twilight..."_

_"What were you talking about?!" she called out._

_"Twilight..."_

* * *

"Twilight!"

She opened her eyes and the first thing found herself lying on the polished floor. Twilight groaned and clutched her head while Jonathan moaned next to her. Twilight sat up off the floor and looked at the Doctor, now examining Jonathan's awkwardly bandaged foreleg. The Doctor searched for the end of the bandage so that he could examine it.

"You had quite a scene, there," he said, not taking his eyes off the bandage.

"W-what?" Twilight stammered, "What happened?"

"Telepathic connection. When you touched his head, you shared a thought. It must have been a strong one at that, making you lose consciousness. That's been happening a lot, lately. Ah-ha!"

The Doctor found the bandage's end, he started to unwrap it carefully while Twilight came over to see. He finished removing the bandage, and then his expression turned from that of confusion, to thought, and to realization in a matter of seconds. Jonathan was wearing a leather band around his foreleg, close to his hoof, with a rectangular, metallic device attached to it. The metallic part was mostly different buttons, but there was also a small screen that, at the moment, was black. The strangest part, though, was that it appeared to be a _part_ of his leg. The leather was _burned_ _into_ him, but it had turned the parts of Jonathan's leg around it a light shade of brown.

Twilight was puzzled, "Doctor, what is that thing?"

"That, my dear Twilight," he responded, "is how our strange friend originally got here."

"But... what is it?"

"A vortex manipulator."

"And that does...?"

"It's a rough form of time travel," the Doctor elaborated. "This thing is like a compact TARDIS, without the 'vromp'-ing, of course. Still, it's quite a doozy."

Twilight shook her head, and something caught her eye. "Doctor?"

"Yup?"

"He has no mark."

"And that means?..."

"Just look."

The Doctor sighed, "Alright, what's this big mark crisis?" Twilight pointed to Jonathan's flank and the Doctor examined it at a distance. "So? It's fine."

"No," Twilight said, "It's blank."

* * *

_A/N: BUM-BUM-BA-BUUUUUUUUUUMMMMMMMMMMMM!_

_I love cliffhangers, they keep things suspenseful. A short chapter, sadly. Two weeks and you get this. I hate Writer's Block. _

_The next chapter will be appearing who knows when since I have another fic. to take care of and a BOATLOAD of schoolwork. Still, keep your notifications on, I may do some extreme fic. writing this week!_


	4. Slipping Through the Cracks

_**Chapter 3**__**  
**_

_**Slipping Through the Cracks**_

**Gaia; Equestria; Crystal Empire; Crystal Palace; Main Dining Hall; 1 P.C.E.**

"WAIT!" Jonathan screamed as he regained consciousness.

"WOAH!" the Doctor and Twilight shouted as Jonathan shot up.

"DON'T LET IT TOUCH YOU!" Jonathan screamed, "DON'T LET IT TOUCH YOU!"

"Stop," Twilight said to him, "Stop! Jonathan!"

Jonathan slowly ceased his struggling and was breathing heavily. "D-did... did you... see it?!" he asked between breaths, "Whatever it was?!"

"Yes. Yes I did," Twilight replied calmly hoping that he would calm down as well. Jonathan started to do so, placing his hooves over his eyes and rubbing them.

"Actually..." the Doctor started, "What _did_ you see?"

Jonathan looked to the Doctor, his eyes wide open, full of worry. "There was... there was this... _thing_. A creature that sounded, um, male. He... he _knew_ me, about my life. He told me that I wasn't supposed to happen, that I was a mistake." Jonathan looked towards the floor, "He knew about the numbers."

"What about the numbers?" the Doctor urged, "Tell me."

"Four, one, eight, three, zero," Jonathan said, head still lowered.

"Four, one, eight, three, zero," the Doctor repeated in a whisper.

Twilight turned to the Doctor, "Is that important?"

The Doctor nodded silently. "On my way here in the TARDIS," the Doctor began to explain, "the monitor on the console showed those numbers, but they disappeared shortly after."

"And you think that Jonathan knows what they mean?" Twilight asked.

"Perhaps."

"Just perhaps?" Twilight said doubtfully, "That's it?"

"Mmmm... yes."

"Have either of you seen my book?" Jonathan asked, looking around. "I thought I had it."

Twilight spotted it on the floor a few feet away. "There it is." She went over, picked it up, and returned it to Jonathan. He quickly flipped open the book and stopped on a page that held only one line of writing: '_Left;_ _42, 38, 10; Up; 40, 16; Left; 18, 38; Blue; 38, 10, 40.'_

"Twilight, could you hang on to my sonic screwdriver for me?" He tossed it over when she nodded, catching it with her magic and storing it magically. "Now, I need to read this." The Doctor spent a few moments going over the writing before closing the book and giving it back to Jonathan. "That's good!" he shouted before rushing to the large exit doors.

"Wait!" Twilight hurried up to him, Jonathan, book on his back, close behind.

The Doctor pushed open the doors and jumped back when he saw the group of four Vashta guards in front of him. "Sneaking up on people-"

"Ponies," Twilight corrected.

"-ponies -thank you Miss. Sparkle- is _very_ rude!" the Doctor scolded.

_"You will come with us,"_ one of the guards ordered, ignoring the Doctor's comment.

Twilight and Jonathan yelped as two of the guards disappeared and then reappeared behind them. The forward two began to proceed down the corridor, the three ponies, reluctantly, following close behind.

**Gaia; Equestria; Crystal Empire; Crystal Palace; King Sombra's Royal Suites; 1 P.C.E.**

The doors to Sombra's chamber opened inward and the Doctor, Twilight, and Jonathan trotted in silently. The room they were in was entirely black crystal from floor to ceiling. Even the the enchanted torches had been made to give off black flames, though still providing a light source. Sombra stood straight at a window, looking outward over the Empire.

"Doctor," Sombra said, without turning around.

"King Sombra," the Doctor responded.

"You may be wondering why I need you here."

"Not really," the Doctor said thoughtfully, "I was actually thinking about apples. And grass. Perhaps apple-grass. I do love apple-grass! New New York is covered with it. I wonder what it tastes like, being horse and all."

"New new what?" Twilight asked confusedly.

"Long story, good for another time, I'll explain later." Twilight rolled her eyes at the Doctor's response.

"Silence!" Sombra demanded, now turning to face them. "This conversation is irrelevant."

"I was talking!" the Doctor retorted.

"Well, I'm the KING!" Sombra shouted, "and my word is LAW!" He stomped his forehoof on the ground and the entire chamber shook.

"ALRIGHT!" Twilight, Jonathan, and the Doctor screamed in unison.

The room stopped trembling and Sombra addressed his guards, "Take them to the tower."

"Wait, wait, wait!" the Doctor shouted. Everyone looked at him, waiting for whatever he was about to do.

"What?"

"Just tell me one thing," the Doctor pleaded, "How did you get control of the Vashta Nerada?"

"Ah, yes. The guards," Sombra said thoughtfully. "I've grown quite fond of them since their arrival."

"Arrival?"

"Yes," Sombra repeated, "Arrival. My minions were lost. Floating in the infinite darkness. They were crying out. Alone." A dozen of the guards formed behind Sombra, their armor glinting in the black torchlight. "I rescued them."

The Doctor, who had been listening with a great amount of interest, opened his mouth to speak, "You _rescued_ them? And what is this 'infinite darkness?'"

_"The Master brought us here,"_ each guard spoke at the same moment, their voices merging into one. _"We were wandering through the emptiness. The great divide in space. We serve the Master, for he is our rescuer. And soon, he shall rescue our waiting brothers."_

"As you can see, Doctor," Sombra continued, "I am their god!"

"I met someone who called himself a god, once," the Doctor said, "and he was destroyed." The Doctor's voice grew quiet as he finished the sentence, and Twilight watched him look to the side briefly.

"Well, that was too bad for him," Sombra joked. "Now you will do as I instruct."

The guards watching the Doctor and his companions pushed the three of them into the center of the room and encircled them in shadow. Sombra then stepped in front of the Doctor and looked to the ceiling. Suddenly, the floor of the room shuddered and a circular patch of the floor the four of them were on began to lift away from the room. The ceiling opened up and the floor elevated through it. They stopped and were now inside of a smaller crystal structure that was more of a gazebo with a large crystal spire in the center, pointing to the sky. It pulsed with magical energy and briefly fired a beam of light into the sky every couple dozen seconds. Each burst made a single Vashta Nerada creature shoot down from the clouds and appear inside the tower.

"Doctor," Twilight leaned towards him, "what is that thing?"

The Doctor simply stared at the spire and muttered, "No, no, no, no, no..." again and again.

"What is it?" Twilight repeated her question, an extra amount of urgency added to her voice.

"It's a rift machine," the Doctor's voice was grave as he stared at the spire.

"And that does?"

"A rift is a gap in time and space, invisible to the naked eye, but it's like a long scar," the Doctor began to explain, "and sometimes the odd object passes through, like driftwood. It also bleeds energy, rift energy, that the TARDIS can use as a sort of fuel. But, if you widen that scar, anything from anywhere and anytime can fall through, be it good or bad." The Doctor continued to stare at the spire, wondering how it got here and what Sombra wanted with it, "And I'm sure that whatever Sombra wants with it is _bad_."

As if on cue, Sombra stepped towards the machine, "I want you, Doctor, to open that rift up there to retrieve the rest of my soldiers."

"No," the Doctor replied sternly.

Sombra's head whipped around with frightening speed. "What?" he growled, his voice calm but layered with rage.

"I said no."

"And why is that?"

"What you're asking is almost impossible and beyond dangerous," the Doctor said. "Trying to open a gap wider than what you've already done could possibly destroy about four fifths of the universe."

Twilight cocked her head, "Four fifths?"

"Yes," the Doctor confirmed, "four fifths."

"If you won't work willingly," Sombra's eyes began to glow green, "then I'll just need to persuade you." A group of guards quickly encircled Twilight and Jonathan, singling them out. The Doctor could only watch as the inky blackness of the shadows enveloped the two ponies, hiding them from view.

"Doctor!" Twilight's voice was muffled as she cried out, "Doct-" and she was cut off. The shadows that had enveloped her and Jonathan sank into the ground, leaving where the two had been standing empty, but Jonathan's book was still there.

The Doctor whipped his head around to face Sombra. "WHAT HAVE YOU DONE!?"

Sombra's eyes returned to normal, "Nothing... yet."

"Let them go, RIGHT NOW!"

"Only if you fix the machine!" Sombra insisted.

The Doctor's expression changed, slowly, from intense rage to slight sadness. "I'll do it," he said dejectedly.

"Ah-ha! Good! Now, get to work."

"Only..." the Doctor hadn't finished.

Sombra groaned, "What?"

"... only if you return them to me."

"I'll think about it."

"If you don't, then forget it," the Doctor said. He was taking a big risk, putting Twilight and Jonathan's lives in the balance.

The Doctor's hearts raced as he waited for Sombra to think it over. "Alright, then." Sombra's eyes glowed and a column of shadow appeared next to the Doctor. When it receded, Jonathan was standing in its place, dizzy and disoriented.

"Wha-? What just happened?" he muttered before falling to the ground, eyes spinning in their sockets.

"And Twilight?" the Doctor glared.

"After you finish the job," Sombra responded with a glare of his own. Sombra, flanked by his guards, began to descend on a separate patch of floor. "You have twenty-four hours," the king added before the open spot solidified, as if the floor had been there earlier.

The Doctor watched as the tower was encased in a dull grey barrier that pulsed with magical energy. "He underestimates me," the Doctor thought aloud.

"Is that a good thing?" Jonathan asked, now standing back up.

"In our case, yes. In his..." the Doctor paused for a moment, "... not so much." The spire pulsed again, another blast shooting through the dark, swirling clouds. The Doctor approached the rift machine and ran his hooves down the sides. "This device is magnificent," he gawked, "I've never seen anything like it!"

Jonathan came over, book balanced carefully on his back. "What does he, um, Sombra, want you to do with it? Exactly?"

The Doctor continued to examine the spire, feeling along the outside. "A rift machine can open the rift that I mentioned earlier, but you can't usually control what falls through. This machine, though, is paired with magic, that beam that shoots out is apparently magical energy that is being focused on one specific time an place. I've never seen anything like it? It's brilliant!"

"Can you explain it in lay-mares' terms?"

"This machine is opening _another_ rift in a completely different time and place. The Vashta Nerada are being pulled out of that point and are being brought here, to this point." The Doctor completed his examination of the spire, "Sombra want's me to allow _all_ of them to be brought here at once, but there's a reason that I said that it's impossible. The rift is very delicate and can occasionally collapse in on themselves, destroying entire cities. That nearly happened to me once."

"I heard the 'destruction of the universe' part earlier, but now it's only 'destruction of a city?'" Jonathan asked quizzically.

"Well, that was before I examined this, and, I'll say it again, it's brilliant!" The Doctor kicked the side of the spire and a square access panel opened in the side. "There we go." Inside of the hatch was a jumbled mass of wires and small, blinking, multicolored lights. The Doctor rubbed his hooves together, "Oh, you _beauty_!" the Doctor fit the entire front half of his equine body inside of the machine, leaving his lower half hanging out the opening.

"So... you're going to help him?!" Jonathan was dumbfounded.

The Doctor eased himself out of the hatch, gripping a set of wires in his mouth. "No, I'm not," he replied. "All I'm doing... is biding my time."

"But how?! Twilight's still captured, we're being held inside of a magical bubble until you unleash an army, and I'm trying to figure out why I'm trusting you so quickly!"

"I'm a very trustworthy pony." The Doctor smiled and laughed, "I remembered to say 'pony!' Ha! Oh, and Twilight's not captured, just held up."

"What?"

"Did you remember that I gave her my screwdriver?" the Doctor smiled mischievously.

* * *

_A/N: I apologize for the wait and my writer's block was hell. Still, another cliff-hanger for you none the less. What has happened to our dear companion Twilight? Stay tuned!_


	5. Sudden Revelation(s)

_A/N: All I can say is sorry for the wait._

* * *

_**Chapter 4**_

_**Sudden Revelation(s)**_

**Gaia; Equestria; Crystal Empire; Crystal Palace; Location Unknown; 1 P.C.E.**

"LET ME OUT OF HERE!" Twilight screamed. The chains pulled tight against each of Twilight's legs, preventing her from moving much, but her mouth had been left unconfined, allowing her to scream and shout to her heart's content. "DOCTOR?! HELP!" Twilight fired every spell in her arsenal at the metal bands, but nothing worked and only left her coughing on the smoke from the magical feedback.

_"You can try as hard as you wish,"_ a Vashta Nerada guard that suddenly appeared before her said, _"those bonds are meant to withstand any magical output you may cause. Dark magic included."_

"Shut up!" Twilight shouted, firing a blast of magic that passed through the guard. The shot left a hole that slowly reformed after a few seconds. Twilight wasn't sure, but she thought that the guard snickered under its mask.

_"I'll leave you to your thoughts,"_ the guard rasped, dissipating immediately after. The guard reappeared briefly, _"All units may cease guarding the prisoner, orders of King Sombra,"_ and then vanished again. A collective _'Woosh!'_ sounded as all of the guards that had been hidden dissolved into the air.

Twilight cast an illumination spell, lighting up her cell. It was hewn out of pure, black crystal and stretched twenty feet into the air, the ceiling coming to a point at the top of the room. The lavender unicorn looked around, glancing back and forth, checking to see if any guards remained. A small burst of light lit up the air next to her and, as it dimmed, revealed the sonic screwdriver. "Thank you, Doctor," Twilight said, "If magic won't release these cuffs, then maybe science will!" Twilight maneuvered the device down to the locks, pointing it directly at them. The sonic gave out its signature whine, the metal cuffs clicking open almost instantly.

"Yes!" Twilight cheered quietly, setting to work on removing the rest of the chains. When she was free, Twilight pointed the screwdriver at the walls, searching for the door. She turned slowly while the screwdriver whined, its blue tip illuminating the chamber slightly. The pitch increased, suddenly, and a prominent _THUNK _was heard as a portion of the wall swung open slightly. Twilight ran over to the crack and left the room, screwdriver magically grasped next to her. She then found herself in another hallway, illuminated by the enchanted torches that burned with bright green flames.

"Now, what next?" she asked herself. "I should find the Doctor. Then we'll just get back to the TARDIS and-" Twilight stopped. _The TARDIS!_ she groaned mentally. She tapped her muzzle with the screwdriver, contemplating her next move. She stopped again and looked at the screwdriver in her magical aura.

_"Wait. How are we going to find the TARDIS, exactly?" Twilight had asked the Doctor._

_"There's a tracking device inside of the TARDIS that is connected to my sonic screwdriver. With this thing, I'll never lose the TARDIS. It's even more useful when I forget where I park!"_

"Let's hope that the Doctor was telling the truth." The tip illuminated and the whine pierced the unnaturally still air. Twilight pointed it down the near endless hallway and the screwdriver's pitch increased like it had with the door. "Yes," she cheered quietly. She held the levitating sonic in front of her and galloped down into the now less-threatening darkness.

**Gaia; Equestria; Crustal Empire; Crystal Palace; Castle Spire; 1 P.C.E.**

"What does that sonic screw-whatzit do anyway?" Jonathan asked the Doctor.

The Doctor was practically swallowed up by the rift machine, only his brown, shaggy tail visible out the access compartment. He had found that the inside was meant to be large enough, for a pony a bit larger than himself, to do some maintenance without messing up the wiring. "In answer to your question," the Doctor said, "it's primary use is to lock and unlock doors, undo screws and sometimes rivets, as well as a sort of beacon to locate the TARDIS in the event that I lose it. Being that it has happened to me quite a few times."

A flurry of sparks erupted from within the machine and Jonathan jumped back in surprise. "Ah-ha!" he heard the Doctor exclaim. A second cluster of sparks erupted from the inside and the Doctor yelped in pain. "Blasted piece of junk." A gong-like sound emanated as the Doctor kicked the metal inside.

Jonathan backed away slowly and started to look up at the machine in wonder. He walked around the outside of the crystal-encased spire, observing the mirror-like surface and trying to see if he could glimpse the metal exoskeleton of the device. He felt out of place here, not just on the top of a mad-pony's castle in the middle of an entire kingdom made of crystal, but out of sync with the world in general. He didn't dwell long on these thoughts, as a small, black shape caught his attention. Upon closer inspection, he saw that it was painted on the outside of the machine and nearly impossible to spot because of the crystals' natural polish.

"Doctor?"

The Doctor stuck his head out and looked to his right, only seeing Jonathan's tail from around the curve. "What is it, my friend?"

"Come see this," was his reply.

The Doctor shrugged and navigated his way out of the machine, avoiding any important wires and cords. He finally made his way out, stepping out through the access door and stretching his joints. A loud crack resounded from his neck as he twisted it, causing him to grunt in satisfaction. He then trotted over next to Jonathan. "What was it you wanted?"

The grey pegasus simply pointed to a spot on the machine and the Doctor approached the designated place. The shape that he saw inside looked to be in the shape of a relatively large "A" with an open eye residing within the enclosed, upper space of the letter. The symbol, itself, was enclosed within a tall, rectangular box. Below the symbol were the words "_Puto. Creare. Assequendum._"

"'Think. Create. Achieve.'" the Doctor said quietly to himself.

"What was that?" Jonathan inquired. He looked back to the words and was startled to see that he could now read them clearly. 'Think. Create. Achieve.' Jonathan leaned in towards the Doctor and whispered, "I can read that!"

"It's a gift of the TARDIS," he explained, "It takes a bit for it to translate the written word."

"So... I'm reading Latin?"

"Yes, you a-" the Doctor stopped, "How do you know that it's Latin?" he asked curiously, a small hint of suspicion mixing in.

Jonathan shrugged his shoulders, "It just looks like Latin."

The Doctor studied him with increased interest. Jonathan ignored his staring and looked back at the symbol, this time feeling slightly drawn to it. He reached up his right fore-hoof and touched the spot on the crystal that covered it. When his hoof made contact with the crystal, a thin tendril of blue electricity flowed through the glimmering solid and sparked against him. Jonathan instantly froze. His pupils shrank, his wings flared out, and his mane and tail stuck up a bit. The Doctor cocked an eyebrow at the sight.

"21, 9, 6; 2, 19, 4, 9, 10, 21, 6, 4, 21, 20," Jonathan's mouth barely moved when he spoke, though each number was enunciated clearly and quickly. The Doctor mentally recorded the numbers and stored them in an imaginary filing cabinet in his brain. Jonathan stood there in silence for a while before his pupils returned to their normal state, as well as his mane, tail, and wings. "So that's it."

"What?" the Doctor asked, his voice now containing quite a bit of concern.

"My name isn't Jonathan," he responded calmly. He faced the Doctor slowly, his expression was "It's Farsight."

**Gaia; Equestria; Crystal Empire; Crystal Palace; Lower Dungeons; 1 P.C.E.**

Twilight ducked behind a crystal outcropping in the ground as a pair of the shadow guards drifted down the hall. She had been using the screwdriver in bursts to avoid being detected by those patrolling the castle. She activated it again, scanning in a circle as the pitch increased again, leading to a solid wall. Twilight ran up to it and unlocked the door with the sonic. She entered into a large, dark room, twice the size of the cell that they had started out in, and waiting in the center, was the TARDIS. Twilight smiled and ran for the doors.

"_Going somewhere?_" a voice hissed from within the gloom. A guard suddenly appeared in front of the TARDIS, blocking Twilight's path to the doors. "_We were wrong to leave you, weren't we?_"

"Not you, again," she groaned angrily. She lowered her horn, setting it ablaze with her reddened magic. "Can't you just give me a break?" She shot a beam of light at the creature, slicing it right down the middle. It dissolved instantly but it reformed almost as quickly.

"_You are starting to get on my nerves. If I even had any._"

Twilight grunted, "Just go away!" She shot another blast, this one encasing the guard completely. When the light dispersed, the guard was gone, but again he reappeared, now closer to Twilight.

"_Give up,_" he said. "_You can't kill me._"

Twilight was furious now, and her horn sparked with even more energy. "I will _never_ give up!" she shouted at him. Her horn glowed brighter, a small circle of illumination surrounding her form.

The guard raised an eyebrow at the sight.

"I think it's time that you saw the true light of day," Twilight said. Her eyes glowed white with anger and the light from her horn increased dramatically, the circle expanding outwards, enveloping the room in a blinding light.

When the light dimmed and Twilight could see again, she found that the space had now been fully illuminated and the guard was gone. There were some small patches of fire scattered about the room, their light flickering against the stark blackness of the walls. She then turned her attention to the TARDIS which was, surprising to Twilight, completely unscathed. Twilight approached the doors carefully and stopped where the guard had been previously. All that was left of him was a small, star-shaped scorch mark staining the floor.

Twilight looked back at the TARDIS doors and attempted to push them open, unsure if it was locked. Luckily, they swung open with a creak and she trotted inside. She approached the controls and was ready to use the ship, but then she realized:

She had _no idea_ how to fly it. She kicked the console in anger, and a projection of the Doctor appeared on the catwalks above.

"This is emergency protocol 9-20," the hologram stated. "The TARDIS and I have been separated because of some outside force and you are now tasked with returning it to me." The form flickered out and reappeared next to Twilight. "Follow my precise instructions and the TARDIS shall return to my location." Twilight nodded, but she was suddenly confused. "Did I just respond to a recording?"

* * *

_A/N: I finally have enough time on my hooves to focus on writing the final chapters of this episode. I'm hoping to get the next chapter up within the week, but I'll see if my muse permits it._


	6. Bridging the Gap

_**Chapter 5**_

_**Bridging the Gap**_

**Gaia; Equestria; Crystal Empire; Crystal Palace; Castle Spire; 1 P.C.E.**

The Doctor worked on the inside of the rift machine for another few hours, unsure exactly how long he and Jonathan -sorry- _Farsight_ had been up there. He held his sonic screwdriver tightly between his teeth and held it up to a pair of split wires. Slowly, the wires melded together and became one long cord. The Doctor wiped the sweat from his forehead and went back to the access panel to check on Farsight.

He was sitting down near the edge of the crystal floor, watching the small dots that represented ponies slave away. He watched as the guards would just stare at them, never moving unless one of the ponies stopped working or even tripped. In that case, Farsight would watch painfully as the ponies were harmed, the Vashta Nerada simply touching them to provoke their anguish. Farsight saw a small pony, either a filly or a colt, stumble and knock into a pile of gems, spilling them across the ground. One of the armored guards began to approach the child and he turned his gaze away.

The Doctor watched him turn away and noticed a tear run down Farsight's cheek. He could only guess what the pony was watching, having to have seen it himself not too long ago, but he understood exactly what he was feeling. The Doctor looked to the mishmash of wires and switches inside the machine and back to Farsight. He exhaled slowly and climbed out of the hatch.

"Farsight..." the Doctor approached him slowly, "are you alright?"

Farsight quickly wiped away the tear and sniffed, "I-I'm fine."

"Are you su-"

"I said I'm fine," he insisted.

The Doctor knew that this was not the case, so he sighed and sat down next to Farsight. "What's wrong?"

The pegasus was silent for a few moments. "Everything," he finally admitted. "And I know that I've said this who knows how many times, but..." he shook his head, "... it all seems so surreal. I'm just... really overwhelmed."

The Doctor tried to give Farsight a reassuring pat on the back, but he pulled away.

"I don't need sympathy," he explained, "I just need an explanation."

The Doctor stood back up, "Then an explanation will be found!" He held out a hoof to Farsight and he accepted with a hint of reluctance. "Now the first thing," the Doctor started, pointing at Farsight's left leg, "is that vortex manipulator."

**Gaia; Equestria; Crystal Empire; Crystal Palace; Lower Dungeons; TARDIS; 1 P.C.E.**

"Adjust the calibration of the thermal output parameters," the Doctor hologram instructed.

"And that would be...?"Twilight asked.

"The large red lever on the right," it clarified.

Twilight slowly pulled the switch down before a subtle _Ding!_ was heard. "Parameters set."

The projection flickered out again and popped up on the opposite side of the control panels. "Activate temporal resonance and adjust the lateral dilation."

Twilight hurried over to the other controls and pressed the buttons it pointed out. The monitor began flashing on and off, the Gallifrean symbols swirling and quickly realigning. "What now?" she asked.

"Pull that lever," the recording instructed, indicating a large, black switch, nearly two feet long. "It will be more difficult in-flight, so you'll have to be ready."

Twilight nodded, understanding his orders. She wrapped her forehooves around the switch and hesitated for a moment. But only for a moment, because the next thing she knew the central piston moved, the TARDIS shuddered, and the engines sounded.

_VVRROOMMP! VVRROOMMP! VVRROOMMP!_

**Gaia; Equestria; Crystal Empire; Crystal Palace; Sombra's Chambers; 1 P.C.E.**

_VVRROOMMP! VVRROOMMP! VVRROOMMP!_

The sound of the TARDIS engines were echoing throughout the castle. It flooded through the corridors, permeated closed doors, and reached King Sombra's ears.

"_**WHAT?!**_" Sombra's voice boomed even louder than the TARDIS, literally breaking doors and shattering any glass within 100 feet. "_I WANT IT FOUND_ _**NOW!**_ _DO YOU UNDERSTAND_?!" he raged to his guards.

"_Yes, Master,_" they bowed their heads.

"_NOW_ **_MOVE!_**" Sombra ordered, "AND MAKE SURE THE DOCTOR NEVER LEAVES UNTIL THE TASK IS FINISHED!"

The soldiers evaporated to fulfill their orders, obeying Sombra immediately. They shot upwards toward the spire, reforming as a large, black mass of darkness.

**Gaia; Eqestria; Crystal Empire; Crystal Palace; Castle Spire; 1 P.C.E.**

_VVRROOMMP! VVRROOMMP! VVRROOMMP!_

The Doctor smiled widely while Farsight looked around in confusion.

"What's that noise?!" the panicked pegasus asked.

The Doctor practically flew over to the rift machine, leaping through the access panel like an acrobat. "That," he said gleefully, "is phase two!" The Doctor ripped out a pair of wires and snapped them together. The rift machine began to glow a dim blue, the inner workings sparking and crackling wildly.

"What are you doing?!" Farsight panicked again.

"I'm doing what our dear friend Sombra asked me," the Doctor explained, now holding the sonic screwdriver between his teeth, "widening the gap!"

**TARDIS; Control Room; =_Year: It Could be Anything!=_**

Twilight hung on to the controls to prevent herself from being thrown to the floor. The Doctor's projection just stood there as if he was immune to the shaking. "What... now?!" Twilight shouted over the noise.

In response, the hologram pointed at a set of switches just within Twilight's reach. "Throw these three to the 'up' position." Twilight nodded and reached up to the controls.

She was an inch away before the TARDIS jolted violently, sending her crashing back into the railings. Twilight grunted as she slammed into the metal poles, the wind being knocked out of her instantly. She opened her eyes and watched the control panel spark and flare up. The Doctor hologram was still standing by the controls, waiting for Twilight to complete the task. Twilight tried to get back to the controls but found that her back leg was caught between two bars. She tried to tug it free, but it was stuck fast.

**Gaia; Equestria; Crystal Empire; Crystal Palace; Castle Spire; 1 P.C.E.**

The Doctor worked at the internal technology, furiously ripping out wires and replacing others. The machinery sparked and fizzed around him, constantly singing his fur and mane. "Work!" he urged the device, "Work for me!" Farsight nervously watched him work, shifting from side to side anxiously.

Suddenly, the platform they were on was covered in darkness. Farsight looked around to find the magic shield surrounding them was dissolving quickly. At the edge of the tower, a wall of Vashta Nerada were using their shadowy forms to block out the sunlight.

Farsight stood by the access hatch, constantly shifting his gaze between the Doctor and the approaching darkness that was the Vashta Nerada. "Hurry, Doctor!" he shouted, "They're getting closer!"

"Are they coming quickly?" the Doctor shouted back.

Farsight risked a glance and was surprised to see that the shadows were actually moving at a snail's pace. He turned back to the hatch, "They're going slowly! Why?"

"Because I'm pretty sure that they know what I'm doing." The Doctor pulled his sonic screwdriver out and held it up to a panel with flashing multicolored lights. He activated the screwdriver and the lights stopped flashing and became solid colors. Just then, a small red lever was revealed as a hinged plate appeared from the circuit board. The Doctor looked from the switch to Farsight, who was looking at the lever with a worried look. "Ready?" he asked him.

Farsight shook his head, "No."

The Doctor's hoof was inches away and he turned back to Farsight. "I'm not either," and he flipped the switch.

The rift machine shuddered, small cracks appearing in the crystal shell that surrounded it. Farsight watched as bits of the gem cracked off and fell to the floor, shattering. The mass of shadow began to swirl and morph, hissing and crackling as it moved. The machine was visibly shaking now, larger chunks of crystal and gems falling to the floor and shattered further. The machine began to give off a light blue glow, and the Vashta Nerada slowed their advance.

"_What is this?!_" the shadows hissed.

**TARDIS; Control Room; _=Year: It Could be_ Anything!=**

The TARDIS shook and shuddered, the controls shooting off sparks again. Twilight tried to free her leg from the bars, but her efforts were proving futile. "What do I do?" she shouted to the Doctor's hologram. Then it hit her (not literally, though you could hurt yourself in a moving TARDIS). Twilight focused on the switches and concentrated her magical energy on moving them. Her horn glowed, as did the switches. With a mental tug, they were flipped to the 'up' position and the TARDIS leveled out.

Twilight took this moment of peace to navigate he leg out of the bars, pulling it free as quickly as possible. Just as she's standing back up, the TARDIS shudders again and the Doctor hologram appeared next to her and looked like he was grabbing the controls. "Activate placement setting 5-36 and throw the lever you pulled at the start."

Twilight used her magic to turn some dials to five and thirty-six, and ran to throw the switch. She grabbed it and began pulling it back to the upright position. It locked itself in place once it was set and the TARDIS made its final few jolts.

"Well done," the recording said as Twilight panted, relieved that she'd landed. "You are now an amateur TARDIS pilot. Thank you for your participation." The image sputtered out and the TARDIS was silent.

Twilight turned her gaze to the doors and stared at them longingly. She laughed and ran for them at top speed.

**Gaia; Equestria; Crystal Empire; Crystal Palace; Castle Spire; 1 P.C.E.**

_VVRROOMMP! VVRROOMMP! VVRROOMMP!_

The TARDIS materialized next to the rift machine, drawing the attention of everyone on the platform. The Vashta Nerada retreated slightly while Farsight stared at it in shock and the Doctor in joy.

"That's more like it!" the Doctor cheered when the ship was fully formed.

_FIZZ-IT! CRACK!_

The Doctor and Farsight spun to face the machine. It was now vibrating rapidly, and the blue glow turned into crackling bolts of electricity that ran up and down the point.

"What's going on?" Farsight asked.

The Doctor watched as a blue beam of electricity erupted from the spire and into the stratosphere, piercing the cloud layer and cutting a hole straight through it. The Doctor and Farsight watched the beam slowly expand outward, engulfing the rift machine and growing closer to them. "Get into the TARDIS, now!" the Doctor ordered Farsight.

The Vashta Nerada were screeching and hissing loudly, moving away from the beam. One of them was suddenly sucked into the light and released an ear-shattering cry of pain as it was instantly engulfed within the beam. The others began retreating away from the light source as quickly as possible, some unlucky shadows being drawn back to the light.

Farsight and the Doctor ran to the TARDIS doors, which were quickly pushed open by Twilight. The lavender unicorn stepped aside to let the two pass by, but the rift machine caught her eye. "What did you _do_?" she asked the Doctor.

"No time to explain," he replied. "Big beam of immense energy approaching!"

Twilight was shutting the doors when the machine creaked and groaned. The crystal breaking off completely and falling to the ground. The device shuddered and the blue beam of light flickered.

"Doctor?!" Twilight called out, "What's happening?!"

The Doctor returned to the doors and observed the machine. "Oh-no!" he breathed.

The rift machine shook and the light began to dim and recede. With a final shudder, the light flickered briefly and then died.


	7. A Bigger Beam

_**Chapter 6**_

_**A Bigger Beam**_

**Gaia; Equestria; Crystal Empire; Crystal Palace; Castle Spire; 1 P.C.E.**

The beam emitting from the rift machine flickered briefly and then died out.

The Doctor and Twilight stood at the TARDIS doors staring in shock. "No, no, no,no!" the Doctor ran to the device and leapt through the still-open access hatch. He began sorting through the mass of wires and technology as fast as he could, never stopping to look outside.

...

The Vashta Nerada that had been retreating from the spire were now turning to face it. There were clicking and hissing noises as they debated to return. One of them bravely moved toward the spire, and realized that there was no more pulling force being put upon them. It turned to the dark cloud and chittered and hissed, informing them of its discovery. Slowly, the rest of the force began to move forward, approaching the tower with extreme caution.

...

Back on the tower, Twilight rushed to the machine and peeked inside the hatch. "Doctor, what happened?!" she asked, fear evident in her voice.

His head popped out of some wires and he turned to the circuit-board where the lever had been. "The reversal overloaded the universal generator, frying the activation panels and preventing trans-temporal retraction."

"In Equestrian?" Twilight asked, fear replaced with frustration.

The Doctor faced her, his expression grim. "It's not turning back on anytime soon."

"Can't you... you know... restart it?"

The Doctor visibly had an "EUREKA!" moment. He started pulling out wires and cables, one very large one in particular, and brought them outside of the device. "Twilight," he addressed her, "take these inside of the TARDIS and place them by the controls. After you've completed that, I need you to stay inside of the TARDIS with Jonathan, no, _Farsight-_"

"Who's Farsight?" Twilight asked, her head tilted in confusion.

"Farsight _is_ Jonathan. Long story, good for another time," he chattered. "But make sure you don't leave the TARDIS. And, in the case that I don't come back, press the buttons on the TARDIS labeled 'D dash 4' and you'll be brought back to your time."

Twilight shook her head defiantly, "Oh, no! We are _not_ going without you."

The Doctor released the wires and stepped out of the hatch, leaving him standing directly in front of Twilight. "Please. I don't want to suffer any more loss in my life." He and Twilight briefly made eye contact, they watched each other for a moment.

"So old," Twilight muttered, her eyes seeming distant.

"What?" the Doctor pulled back half a step and gently raised an eyebrow.

"Your eyes," Twilight explained, her voice very low, "they look so old. So... tired..." she trailed off.

The Doctor smiled sadly, "I know. Now, hurry. Please."

Twilight's expression changed to sadness, understanding, and then to compliance. "Only if you promise to come back with us."

The Doctor's forlorn smile remained, "I promise."

"Really?"

The Doctor chuckled softly, "Trust me."

Twilight cracked a small smile, "Alright." With a glow from her horn, the wiring was instantly hovering next to her. "Oh," she stopped and face the Doctor, "Here's your screwdriver." A brief flash of light appeared next to her and revealed the sonic.

The Doctor smiled and took the screwdriver from the air. He said a quick, "Thank you," before returning to the machine.

Twilight ran back to the TARDIS, wiring trailing behind her. She hurried through the doors and up to the control panel, a shocked and bewildered Farsight standing next to them.

"I-It's bi-big... er..." he stammered.

"... on the inside," Twilight finished, "I know, right?" Farsight nodded viciously.

"What's happening out there?" he quickly asked Twilight, trying to distract himself from the (near)impossibility around him.

Twilight set the wires down in front of the central platform. "I don't have time to explain right now, but you have to wait here."

"Are you sure I can't help?" Farsight asked again, this time a bit of disappointment in his tone.

"I don't think so. Unless you know about astrophysics?"

"Good point."

...

Back outside, the Doctor was knee deep in the structure's core, fishing around in the sea of cables for an unknown object. "I'm inside of a machine capable of extracting objects from across time and space and there's no-" he suddenly tripped, falling face-first onto a metal cube. When the Doctor opened his eyes, his mouth grew into a smile upon realizing what he just fell on. "... sub-temporal pulse generator!" he exclaimed. "Thank you, whoever built this!" The Doctor found a way to remove the cube from the inside of the machine, dropping it on the floor, equidistant from the machine and the TARDIS.

He grabbed a mouthful of wiring and brought them over to the box. He took out his screwdriver again and started to plug the cords in with calculated precision. "... red goes to black as blue meets green..." he mumbled the directions to himself as he worked. He spared a glance at the cloud of Vashta Nerada, nearly forgetting their presence.

The dark, swirling cluster was slowly closing the distance between themselves and the spire, their speed quickening with each passing moment.

The Doctor gripped the screwdriver between his teeth nervously. If this plan didn't work then he had no idea what would happen. He guessed that he'd have to find out.

Twilight poked her head out the TARDIS doors. "What now, Doctor?"

The Doctor acknowledged her by looking up, but returned to the cube. "Plug the largest cable into the output connector beneath the central controls," he instructed her, never looking up from his work.

"And how do I get to that?"

"The grated floors lift up in pieces," he explained, "You need to remove the first cover that's right in front of the main walkway leading to the doors."

Twilight nodded and hurried back inside the TARDIS. With a levitation spell, she raised the grate up off the floor and set it down beside Farsight, while at the same time she floated the cable over to the new space. A few seconds of frantic searching brought her to a large hole, just the right size for the wiring. With a grunt, Twilight forced the cable inside the hole, dozens of small, electric tendrils now racing up and down its length.

One such tendril snaked along the full length of the wire, through the doors and out to the machine. When the electricity reached the tower, the inner controls flickered on and the machine hummed to life. The Doctor briefly looked up from his work to check on the device, noticing the sudden activity. "Almost there!"he shouted joyfully. He returned his attention to the cube, now almost fully covered in wiring.

"All that's left is the-" the Doctor stopped suddenly. "Oh, no!" he said. He quickly pulled out his sonic screwdriver and scanned the cube. Instantly, a square-shaped panel popped off the top and a well-sized keypad was revealed. It contained the standard ten-digit layout, but a directional pad had been placed below the keys. "Why couldn't this come with a user's manual!" the Doctor complained loudly. The Doctor controlled his breathing and closed his eyes in concentration. He realized that the box was asking for a pass code, the system regulators being locked in the case of foul play.

"The main circuit comes together at twenty... one different points on each side of this cube, making a total of forty-two." He took his hoof and carefully pressed '4' and '2' on the keypad. "Then, the thirtieth cable is opposite number eight." He pressed '3' and '8' now, holding his breath. "I removed five from fifteen," that's '1' and '0' clicked in. Then the Doctor realized something: he'd seen this order before. His face became scrunched up in concentration and he tapped his head with his other hoof. "Think, think, think." His head shot up and his eyes widened.

_He quickly flipped open the book and stopped on a page that held only one line of writing:_ _'_Left; 42, 38, 10; Up; 40, 16; Left; 18, 38; Blue; 38, 10, 40.'

The Doctor clapped his hooves together. The numbers were the key! "Thank you, Farsight!" The Doctor proceeded to input the remaining numbers: '40, 16, 18, 38, 38, 10, 40.' He hit the last zero and the cube buzzed to life. "Yes!" the Doctor cheered. His celebration was cut short as the cube suddenly stopped humming.

"What?!" the Doctor whined, "What now?!" He replayed the message in his head again: _'_Left; 42, 38, 10; Up; 40, 16; Left; 18, 38; Blue; 38, 10, 40.'

The Doctor looked back at the keypad and remembered the arrow keys. "There we are!" He pressed the keys: left, up, left. Then, he stopped. The Doctor examined the box, checking each side carefully, but nothing that was blue revealed itself. He groaned in anger, "Really?!"

He looked out at the mass of Vashta Nerada, continually picking up speed as they neared the tower. He massaged his eyes with his hooves and let out an exasperated sigh. He realized that he couldn't restart the rift machine without the box, knowing that any other method would destabilize the time stream. The Doctor turned back to the TARDIS and considered his options: he could either try to restart the system without the cube, but that would take hours, time that they didn't have. The other option was one that he had been choosing for a long, long time: run.

The Doctor continued to stare at the TARDIS, that little blue box was the only bright color in this darkened-. _Blue box_, the Doctor thought, his eyes growing wide with realization. _The _blue box! the Doctor knocked his forehead with his hoof. "I really need to practice thinking under pressure!" he scolded himself.

**TARDIS; Control Room; 1 P.C.E.**

Twilight stood around the controls, running her hoof along the different levers and switches. She had found the 'D dash 4' setting a while ago, but was holding off until the Doctor returned.

"How long do we wait?" Farisght asked Twilight, breaking her out of her semi-trance.

She opened her mouth to answer, but the TARDIS doors beat her to it. The Doctor stood at the doorway, smiling from ear to ear, the cube sitting on his back. "You'll be waiting for no longer!"

Twilight perked up immediately, "What is it, Doctor?! Are we ready?"

"Almost," he said, making his way to the lower wiring and dropping the cube. "All I need is to strengthen the temporal feed and this thing will be up and running, giving us time to save this place from the Vashta Nerada and shove off without a scratch!"

"It's that easy?" Farsight asked.

"Indeed!" The Doctor propped the cube up against the TARDIS and connected it to the console.

"How is it going to work?" Twilight inquired.

"The TARDIS is a time machine, remember? By hooking the rift machine up to it, I'll be able to boost the energy and return those shadows to their appropriate place!" The Doctor ran from control to control, flipping switches and spinning dials, caught in his own world. As he worked, the metal cube began to glow blue, the light gently illuminating the space. "Twilight?" he called.

"Yes Doctor?"

"When I say go, I need you to flip this," he pointed to a red handled lever, "into the up position, alright?"

Twilight nodded, "I've got it!"

"Perfect!" The Doctor ran back to the still-open TARDIS doors and checked on the Vashta Nerada. They were less than twenty feet away from the tower and closing the gap quickly. "Ready Twilight?"

"Ready!" she confirmed.

Fifteen feet...

... Ten...

"And..." the Doctor started.

... Five...

"NOW!" he shouted at the top of his lungs.

Twilight immediately flipped the switch and the cube began sparking with electricity that ran through the cables and flowed along the main one. The power shot out the doors and reached the machine, engulfing it in electricity. The machine's blue glow returned stronger then ever now, covering it with near-blinding light.

"_WHAT IS THIS?!_" the demented hissing of the Vashta Nerada reverberated throughout the tower.

Suddenly, the spire shot its beam back into the sky and sliced a hole in the clouds. Once again, the Vashta Nerada were being pulled towards it at a tremendous rate. As each one of them touched the light, it disappeared with an earsplitting screech. The mass of the creatures began to decline as each was absorbed by the rift, their numbers dwindling each second.

Bolts of lightening assaulted the interior of the tower, scorching the crystals in their wake. The Doctor watched the darkness of the Vashta Nerada as they disappeared from this time, being blasted back to their own. He saw them desperately trying to escape its gravitational pull, their efforts ultimately in vain.

"_**DOCTOR!**_"

He spun his head around and looked to the edge of the tower floor. Sombra stood there and glared at the Doctor with pure rage and hatred.

"_**I'LL KILL YOU FOR WHAT YOU'VE** **DONE!**_"


	8. A Different Kind of Magic

_**Chapter 7**_

_**A Different Kind of Magic**_

"_**DOCTOR!**_" Sombra screamed at the top of his lungs.

"Oh, dear," was his only reaction.

Sombra's horn glowed with dark energy and a black magical aura surrounded it. "You will suffer, Doctor!" he seethed.

The Doctor looked nervously to the spire. Nearly all of the Vashta Nerada had been absorbed back into the rift but there was still a few of them to go. All he needed to do was stall. The Doctor inhaled deeply and exhaled slowly, taking a step out of the TARDIS.

"Doctor!" Twilight called from within, "What's happening?"

He turned to face the pair of ponies in the TARDIS, "I'm sorry," he said to them. He then pulled out his screwdriver and activated it. The doors to the ship snapped shut and locked themselves, locking Twilight and Farsight in, and the Doctor out. He turned back to Sombra and exhaled. "I suppose that you're going to kill me now?"

"Indeed," Sombra snorted, "I've always wanted to destroy a god, and I suppose that you will suffice." He scraped his hooves across the crystal floor, using enough strength to create impurities in its surface.

The Doctor readied himself, spreading his hooves in what he hoped looked like a defensive stance. He lowered his head but his eyes never left Sombra. "Allons-y," he breathed.

Sombra charged at the Doctor while the latter pulled out his sonic screwdriver and charged as well.

**In the TARDIS**

Twilight pounded at the doors with all her might and screamed, "DOCTOR!" She realized his plan once Sombra reached the tower, and she knew that he would most likely be killed if her tried to fight him. "DOCTOR!" she bucked the TARDIS doors, eliciting a vibrating hum from the ship. Twilight grinned sheepishly. "Sorry," she apologized.

Farsight, who had been leaning on the control platform's guard rails, tilted his head in confusion. "Did you just... apologize to the ship?" he asked dumfounded.

"The ship's alive, according to the Doctor," she explained. "He'll probably explain it in greater depth later." Twilight returned to the doors and battered them mercilessly.

**Outside Again**

During his charge, Sombra shot a blast of dark energy at the Doctor's legs, meaning to disrupt his own advance. The Doctor, on the other hoof, shifted to the left and dodged the attack, his pace never faltering. Sombra growled and fired more blasts, the Doctor managing to dodge each one of them successfully.

The two of them were just about to collide when the Doctor suddenly jumped to the side, startling Sombra and avoiding his advance simultaneously. The Doctor spun around, impressed with his newfound agility as he aimed his screwdriver with his teeth. Sombra slid to a halt and spun around as well.

"Don't make this harder than it needs to be, Doctor!" Sombra shouted. "I bear the arms of dark magic." To prove his point, Sombra's horn glowed black, and a patch of black fire surrounded the tower, cutting off the light of whatever sunlight could be seen through the thick clouds.

With a loud whine, the screwdriver's tip illuminated the now pitch black space. "Well, I bear the arms of... sonic tools!" the Doctor retorted over the noise. "I need something better then that," he quietly scolded himself. Suddenly, the dark fire surrounding the tower began to die out.

"What is this?!" Sombra stared in confused rage. He turned to the Doctor and he saw the sonic screwdriver in his mouth, still glowing. "What sort of sorcery is this?!"

"Huh?" the Doctor cocked his head.

"Your wand!" Sombra growled, pointing at the screwdriver. He shot a beam of dark magic at the Doctor in an attempt to destroy the strange device.

The Doctor saw the beam coming a second too late and braced himself.

**TARDIS**

Twilight was leaning against the doors in defeat, mumbling quietly to herself. Farsight stood at the controls, examining the TARDIS more thoroughly.

"How did he get the inside through the outside?" he asked to nopony in particular. Twilight moaned. Farsight turned to her, "What's wrong, Twilight?"

"Hnm Ommner," she mumbled.

"What?"

"It's over," she repeated a bit louder.

Farsight looked at her like she was a filly that had just eaten something disgusting. "Over?" Twilight nodded slightly at the question. "Over?" Farsight repeated, "You're giving up?" Twilight turned her head away from him this time. "You can't just give up! You two are almost unstoppable together."

Twilight stared at him, not expecting this newfound courage to come from him. "What's gotten into you so suddenly?" she asked quizzically.

Farsight snorted and trotted down the walkway to the doors. "Why are you giving up?!"

Twilight sputtered out a quick, "Because... it's hopeless."

"Define hopeless," Farsight glared at her.

"Sombra's too powerful," Twilight elaborated. "My friends and I have faced him before, and even when he was at half of his normal strength he nearly beat us. Still, I can't help the Doctor even if I wanted to, the doors are locked if you hadn't noticed."

Farsight stepped beside Twilight and checked the doors. She was right, they were locked in place. _'There's no way to open thes- Wait a minute,'_ Farsight cought sight of a small, metal bolt between the doors. He took the small handle in his hoof and pulled it aside, receiving a strong *_click_* in response.

Twilight quickly stood back up and stared at the doors before giving Farsight a sheepish grin. "Heh-heh, that was... easy."

Farsight just cocked an eyebrow at her, "Really?"

**The Tower**

Sombra's dark magic raced towards the Doctor, sparking and crackling with power. He braced himself, anticipating the impact as the magic reached him.

_FIZZIT!_

The Doctor cracked open an eye, then the other. He waited for some indication of intense pain, even the strange, warming feeling of regeneration.

No such feeling came.

He stood there and examined his body, unsure of what he was actually looking for. As far as he was concerned, he was fine.

"**_WHAT?!_**" the sound of Sombra's rage shocked the Doctor back to attention. The Crystal King was glaring at him with unrelenting fury. "_HOW?!_" Two more blasts shot out of his horn and raced to the Doctor.

This time, the Doctor watched the magic come for him, and just as the beams reached him, they fizzled out and were dissolved into the air. He blinked in intrigue.

"What is that device?!" Sombra pointed, once again, at the screwdriver. "How is that magic possible?!"

The Doctor looked down at the sonic, just realizing that it was still activated and whining. "Fascinating!" he cried out. It appeared that the screwdriver had somehow protected him from harm. He looked back at Sombra and smirked. Slowly, he started to advance towards the black unicorn.

More magic was fired at the Doctor, but the sonic deflected them effortlessly. The chestnut stallion continued forward, his invisible shield holding danger back. "Last chance, Sombra!" he shouted, "Stand down and I'll leave you in peace!"

A growl was Sombra's response, "NEVER! I SHALL DESTROY YOU!" The King began to charge the Doctor with his horn lowered threateningly. The distance between the two of them was closing fast.

Thirty feet... twenty feet... fifteen... ten...

"**_NO!_**"

The shout rang out, startling both Sombra and the Doctor. Suddenly, a grey form crashed against Sombra, knocking him away. The impact knocked the wind out of the unicorn and the magic he was conjuring shot out of his horn. Sombra hit the floor and slid towards the tall beam of the rift machine, stopping a few inches away from the tower of light.

The Doctor looked at Sombra's assailant, only to find that Farsight had been the cause. The grey pegasus had opened the doors to the TARDIS just as the two enemies were advancing on each other. At the last second, he had run through the doors and thrown himself at Sombra, disrupting his attack. Now, Farsight was standing in the Crystal King's previous position, glaring at him fiercely.

"I won't let you hurt the Doctor," he said sternly.

The Doctor just stared at him in shock, wondering how such a timid pony had become so brave all of a sudden. Before he could answer, though, a subtle rumbling sound began to reverberate across the tower. The three ponies and Twilight, who was standing at the TARDIS doors in the same state of shock as the Doctor, watched the pointed form of the rift machine as it shook violently.

Then, without warning, the beam began to slowly expand outwards.

Sombra watched the light of the machine begin to approach him and he attempted to stumble away, but he was grabbed by something. He turned around and saw that some of the Vashta Nerada that were being absorbed were reaching out to him, preventing him from escaping.

"_MASTER!_" they hissed at Sombra, "_HELP US!_"

Sombra made an attempt to free himself from their grasp, but it was to no avail. The shadows were just too strong. "Get _off_ of me! I demand it!" he ordered them. The shadows didn't seem to listen and refused to relinquish their grip on him, pulling him closer to the beam. Just as he was at his edge, Sombra glared at Farsight. "YOU'VE DONE THIS TO ME! REMEMBER, BOY, YOU'VE DONE THIS TO M-!" and Sombra, with all of his evil, was sucked into the machine.

Farsight stared at where Sombra had been, his expression blank and his eyes glazed over. The beam was approaching him, its speed increasing with each second, but he was completely oblivious. The Doctor ran over to him and pulled him Farsight back towards the TARDIS.

"I killed him," Farsight mumbled, "I killed him." His senses began to return and he realized that the Doctor was dragging him away from the light. He shook off his dizziness and the two of them stumbled over to the ship. Twilight was standing in the doorway, beckoning to them with her hoof.

"Come on, you two!" she shouted, "We have to get out of here!"

The Doctor was the first through the doors followed by Farsight, who collapsed in a heap just inside the ship. The Doctor didn't notice him fall and continued to run up to the controls. When he reached the console, he was met with a terrible sight: the cube that he was using to regulate the beam was damaged severely. The box was smoking and a small hole ran through its center. "No, no, no, NO!" the Doctor pleaded with the box, somehow hoping that it would fix itself. With incredible speed, the Doctor ran from button to lever to dial, adjusting them with immense precision.

Meanwhile, Twilight was sitting next to Farsight, all while he mumbled, "I killed him. I killed him. I killed him..." over and over again. Twilight dared a glance out the still open TARDIS doors.

"Uh, Doctor?!" she said half panicked, "That beam is getting closer!"

"I'm _very_ well aware of that Miss Sparkle!" he answered between adjustments. He grabbed the main lever on the console, "HANG ON!" With a sharp tug, the lever flipped down and the TARDIS shuddered erratically.

Twilight watched out the doors as the TARDIS began to pull away from the tower.

_**KA-KRACK!**_

The cables that were plugged into the TARDIS were ripped out of their sockets and slid out the door, loose wiring flailing behind them. Outside, the beam of light began to envelop the palace, its speed continually increasing. Then, it began to move outward towards the surrounding area. Twilight watched the ponies run away in terror, seeking shelter from the light, but to no avail. The fleeing figures were swallowed up and disappeared. Twilight turned away and buried her face in Farsight's mane, not wanting to watch anymore.

The TARDIS jolted away from the scene, but it dropped out of the sky seconds later. The Doctor wrestled with the controls, slowing their free fall. The ship landed on the ground, nearly a mile away from the city, now just a towering pillar of blue light. The Doctor ran up to the doors and swung them closed, before looking to the ponies next to him. "Brace yourselves!"

Twilight did so immediately while Farsight did the same, though he was only half aware of it. Seconds later, an explosion rocked the exterior of the ship, battering the doors and forcing them open. The Doctor was thrown backwards and landed on top of Farsight, gaining a pained grunt in response.

A few moments passed before the Doctor and the others struggled to their feet. "Are you both alright?" he asked them. Twilight simply nodded while Farsight groaned. "Good." The trio turned their attention to the doors and peered outside. Instead of seeing the Crystal Empire, all that they saw was a vast expanse of Arctic snow.

"What happened to the Empire?" Twilight asked quizzically.

The Doctor gave out a sigh of relief. "It's been absorbed by the rift," he stated, "thrown through time. I wonder where it ended up."

"1000 years in the future," Twilight replied. "I always wondered how they disappeared for a thousand years without any knowledge that time had passed."

The Doctor shot her an approving glance, "Very informative Miss Sparkle. You really must indulge me with your country's past. That, and teach me how to use hooves."

Twilight laughed lightly, "That shouldn't be a problem, Doctor."

The pair then turned to face Farsight. The pegasus pony was rubbing his side with his hoof, trying to remove the pain from when the Doctor fell on him. He caught them staring and returned the action, "What?"

"Are you alright?" the Doctor approached him slowly, "You seem to be having a hard time."

Farsight opened his mouth to protest, but nodded in assent. "Yeah, I... I killed him. Sombra." He stood there in silence for a bit. "I pushed him into the machine."

Immediately, a lavender hoof was wrapped around Farsight's neck. "It's not your fault," Twilight reassured him, "It was the Vashta Nerada. They pulled him in. You didn't do anything about it."

"I still feel guilty about it."

"Well don't," the Doctor chimed in, "You saved countless lives today. I would call you 'brilliant' but since I'm here..." He trotted up to the controls and leaned against them. "As a thank you, I'm going to allow you to choose where we go next." The Doctor's hoof hovered over the controls, ready to do what was required.

"That's nice and all, but..." Farsight started, "could we just wait for a bit, I'm a bit overwhelmed from everything that happened."

"Fair enough," the Doctor nodded slightly. "I'll just set the TARDIS to drift mode. That way, you can have as much time as you need to decide, as well as allow Twilight to teach me how this universe works." He began to input commands into the ship. He stopped working and turned to Farsight, "When you're ready to pick where and whenever you want to go, just let me know." The Doctor flipped the switch.

_VVRROOMMP! VVRROOMMP! VVRROOMMP!_

* * *

_A/N: Woo! I did it! This was (so far) the most difficult episode to write. Anyway, comments and critiques appreciated. __ALLONS-Y!_

COMING SOON . . .

The Whooves Collection Episode Four: A Starlit Wreck


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